

python3 PolyA-miner.py \
         -mode bam \
         -o /sd.lnk/PolyAdata/2P_BAM_result \
         -pa mm9.PolyA_DB.bed \
         -index /tmp/mm9/mm9_index/mm9 \
         -fasta /tmp/mm9/mm9.fa \
         -bed mm9.knownGene_transcript.bed \
         -p 20 \
         -pa_p 0.6 \
         -pa_a 3 \
         -pa_m 1 \
         -ip 30 \
         -outPrefix BamBBAno \
         -c1 /sd.lnk/PolyAdata/2P_BAM_Data/45_CAA.sorted.bam \
         -c2 /sd.lnk/PolyAdata/2P_BAM_Data/46_CAA.sorted.bam \
         -expNovel 1 \
         -t BB

python3 PolyA-miner.py \
         -mode bam \
         -o /sd.lnk/PolyAdata/3P_BAM_result \
         -pa mm9.PolyA_DB.bed \
         -index /tmp/mm9/mm9_index/mm9 \
         -fasta /tmp/mm9/mm9.fa \
         -bed mm9.knownGene_transcript.bed \
         -p 20 \
         -pa_p 0.6 \
         -pa_a 3 \
         -pa_m 1 \
         -ip 30 \
         -outPrefix BamBBAno \
         -c1 /sd.lnk/PolyAdata/3P_BAM_Data/43_CAA.sorted.bam \
         -c2 /sd.lnk/PolyAdata/3P_BAM_Data/44_CAA.sorted.bam \
         -expNovel 1 \
         -t BB